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It was an joint operation of central intelligence and anti-terrorism squad personnel who caught the suspect, identified as Shahrukh Saifi, near Ratnagiri in Maharashtra, he said.
A sketch of the suspect by released by the Kerala Police based on the description given by a witness, the official said.
The Kerala Police officials have reached Ratnagiri and the suspect will be handed over to them for further probe into the incident, he said.
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The bodies of a woman, an infant, and a man, who went missing from the train after the fire, were recovered from the tracks near the Elathur railway station, late on Sunday night. Police believe they fell off the train or attempted to get down after seeing the fire.
A Special Investigation Team (SIT) of the Kerala Police was subsequently formed and it had intensified its probe into the incident.
According to police, the incident was probably pre-planned as he was carrying petrol in a bottle in his bag.